European Biophysics Journal

, Volume 37, Issue 5, pp 573–582 | Cite as

Dynamics of well-folded and natively disordered proteins in solution: a time-of-flight neutron scattering study

Original Paper

Abstract

Casein proteins belong to the class of natively disordered proteins. The existence of disordered biologically active proteins questions the assumption that a well-folded structure is required for function. A hypothesis generally put forward is that the unstructured nature of these proteins results from the functional need of a higher flexibility. This interplay between structure and dynamics was investigated in a series of time-of-flight neutron scattering experiments, performed on casein proteins, as well as on three well-folded proteins with distinct secondary structures, namely, myoglobin (α), lysozyme (α/β) and concanavalin A (β). To illustrate the subtraction of the solvent contribution from the scattering spectra, we used the dynamic susceptibility spectra emphasizing the high frequency part of the spectrum, where the solvent dominates. The quality of the procedure is checked by comparing the corrected spectra to those of the dry and hydrated protein with negligible solvent contamination. Results of spectra analysis reveal differences in motional amplitudes of well-folded proteins, where β-sheet structures appear to be more rigid than a cluster of α-helices. The disordered caseins display the largest conformational displacements. Moreover their global diffusion rates deviate from the expected dependence, suggesting further large-scale conformational motions.

References

  1. Ahmad E, Naeem A, Javed S, Yadav S, Hasan Kahn R (2007) The minimal structural requirement of concanavalin A that retains its functional aspects. J Biochem 142:307–315CrossRefGoogle Scholar
  2. Alaimo MH, Wickham ED, Farrell Jr HM (1999) Effect of self-association of αs-casein and its cleavage fractions αs-casein (136–196) and αs-casein (1–197) on aromatic circular dichroic spectra: comparison with predicted models. Biochim Biophys Acta 1431:395–409Google Scholar
  3. Bee M (1988) Quasielastic neutron scattering. Adam Hilger, LondonGoogle Scholar
  4. Bee M (2003) Localized and long-range diffusion in condensed matter: state of the art of QENS studies and future prospects. Chem Phys 292:121–141CrossRefADSGoogle Scholar
  5. Branden C, Tooze J (1999) Introduction to protein structure, 2nd edn. Garland Publishing Taylor & Francis, LondonGoogle Scholar
  6. Bu Z, Biehl R, Monkenbusch M, Richter D, Callaway DJE (2005) Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy. PNAS 102:17646–17651CrossRefADSGoogle Scholar
  7. Busch S, Doster W, Longeville S, García Sakai V, Unruh T (2006) Microscopic protein diffusion at high concentration. MRS Bull Quasielastic Neutron Scattering Conf 2006:117–116Google Scholar
  8. Dauphas S, Mouhous-Riou N, Metro B, Mackie AR, Wilde PJ, Anton M, Riaublanc A (2005) The supramolecular organization of β-casein: effect of interfacial properties. Food Hydrocolloids 19:387–393CrossRefGoogle Scholar
  9. Doster W, Longeville S (2007) Microscopic diffusion and hydrodynamic interactions of hemoglobin in red blood cells. Biophys J 93:1360–1368CrossRefGoogle Scholar
  10. Doster W, Settles M (2005) Protein–water displacement distributions. Biochim Biophys Acta 1749:173–186Google Scholar
  11. Euston SR, Horne DS (2005) Simulating the self-association of caseins. Food Hydrocolloids 19:379–386CrossRefGoogle Scholar
  12. Fitter J (2006) Conformational dynamics measured with proteins in solution. In: Neutron scattering in biology: techniques and applications, Springer Biological Physics Series, Chap. 17Google Scholar
  13. Farrell JR HM, Kumosinski TF, Cook PH (1999) Environmental influences on the particle sizes of purified kappa-casein: metal effect. Int Dairy J 9:193–199CrossRefGoogle Scholar
  14. Farrell Jr HM, Wickham ED, Unruh JJ, Qi PX, Hoagland PD (2001) Secondary structural studies of bovine caseins: temperature dependence of β-casein structure as analyzed by circular dichroism and FTIR spectroscopy and correlation with micellization. Food Hydrocolloids 15:341–354CrossRefGoogle Scholar
  15. Farrell Jr HM, Qi PX, Brown EM, Cooke EM, Tunich PH, Wickham ED, Unruh JJ (2002) Molten globule structures in milk proteins: implications for potential new structure-function relatioships. J Dairy Sci 85:459–471CrossRefGoogle Scholar
  16. Fischer H, Polikarpov I, Graievich AF (2004) Average protein density is a molecular-weight-dependent function. Protein Sci 13:2825–2828CrossRefGoogle Scholar
  17. Gaspar AM (2005) TOFTOF intensity and resolution functions, technical report, http://www.ph.tum.de/~agaspar/AG_toftofreport.pdf; arXiv:0710.5319v1(physics.ins-det)
  18. Gaspar AM, Doster W, Gebhardt R, Petry W (2006) β-casein dynamics and association: quasi-elastic scattering studies, annual report of the chair E13 of the physics department of the Technische Universität München; unpublished resultsGoogle Scholar
  19. Gebhardt R, Doster W, Kulozik U (2005) Pressure-induced dissociation of Casein Micelles, size distribution and the effect of temperature. Braz J Med Biol Res 38:1209–1214CrossRefGoogle Scholar
  20. Hansen S, Bauer R, Lomholt SB, Quist KB, Pedersen JS, Mortensen K (1996) Structure of casein micelles studied by small-angle neutron scattering. Eur Biophys J 24:143–147CrossRefGoogle Scholar
  21. Holt C, de Kruif CG, Tuinier R, Timmins PA (2003) Substructure of bovine casein micelles by small angle X-ray and neutron scattering. Colloids Surf A Physicochem Eng Asp 213:275–284CrossRefGoogle Scholar
  22. Horne DS (2002) Casein structure, self-assembly and gelation. Curr Opin Colloid Interface Sci 7:456–461CrossRefGoogle Scholar
  23. Kruif CG (1999) Casein micelle interactions. Int Dairy J 9:183–188CrossRefGoogle Scholar
  24. Leclerc E, Calmettes P (1997) Interactions in micellar solutions of β-casein. Physics B 234–236:207–209CrossRefGoogle Scholar
  25. Leclerc E, Calmettes P (1998) Structure of β-casein micelles. Physics B 241–243:1141–1143Google Scholar
  26. Lechner RE, Longeville S (2006) Quasielastic neutron scattering in biology, partII: applications. In: Neutron scattering in biology: techniques and applications, Springer Biological Physics Series, Chap. 16Google Scholar
  27. Marchin S, Putaux J-L, Pignon F, Leonil J (2007) Effects of the environmental factors on the casein micelle structure studied by cryo transmission electron microscopy and small-angle x-ray scattering/ultrasmall-angle X-ray scattering. J Chem Phys 126:045101CrossRefADSGoogle Scholar
  28. O’Connell JE, Grinberg VYa, Kruif CG (2003) Associatin behaviour of β-casein. J Colloid Interface Sci 258:33–39CrossRefGoogle Scholar
  29. Perez J, Zanotti J-M, Durand D (1999) Evolution of the internal dynamics of two globular proteins from dry powder to solution. Biophys J 77:454–469CrossRefGoogle Scholar
  30. Qi PX, Brown EM, Farrel Jr HM (2001) ‘New-views’ on the structure-function relationships in milk proteins. Trends Food Sci Technol 12:339–346CrossRefGoogle Scholar
  31. Sawyer L, Holt C (1992) The secondary structure of milk proteins and their biological function. J Dairy Sci 76:3062–3078CrossRefGoogle Scholar
  32. Sawyer WH, Dabscheck R, Nott PR, Selinger BK, Kuntz ID (1975) Hydrodynamic changes accompanying the loss of metal ions from concanavalin A. Biochem J 147:613–615Google Scholar
  33. Smyth E, Syme CD, Blanch EW, Vasak M, Barron LD (2001) Solution structure of native proteins with irregular folds from Raman optical activity. Biopolymers 58:138–151CrossRefGoogle Scholar
  34. Smyth E, Clegg RA, Holt C (2004) A biological perspective on the structure and function of caseins and casein micelles. Int J Dairy Tech 57:121–126CrossRefGoogle Scholar
  35. Syme CD, Blanch EW, Holt C, Jakes R, Goedert M, Hecht L, Barron LD (2002) A Raman optical activity study of rheomorphism in caseins, synucleins and tau. Eur J Biochem 269:148–156CrossRefGoogle Scholar
  36. Tarek M, Tobias DJ (2006) Subnanosecond dynamics of proteins in solution: MD simulations and inelastic neutron scattering. In: Neutron scattering in biology: techniques and applications, Springer Biological Physics Series, Chap. 23Google Scholar
  37. Unruh T, Neuhaus J, Petry W (2007) The high-resolution time-of-flight spectrometer TOFTOF. Nucl Instrum Methods Phys Res A 580:1414–1422 and erratum 585:201Google Scholar
  38. Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269:2–12CrossRefGoogle Scholar
  39. Uversky VN, Talapatra A, Gillespie JR, Fink AL (1999) Protein deposits as the molecular basis for amylosis. Parts I and II. Med Sci Monit 5:1001–1012 and 1238–1254Google Scholar
  40. Uversky VN, Gillespie JR, Fink AL (2000) Why are ‘natively unfolded’ proteins unstructured under physiological conditions? Proteins 41:415–427CrossRefGoogle Scholar
  41. Walstra P, Jenness R (1984) Diary chemistry and physics. Wiley, New YorkGoogle Scholar
  42. Wong DWS, Camirand WM, Pavlath AE (1996) Structures and functionalities of milk proteins. Crit Rev Food Sci Nutr 36:807–844CrossRefGoogle Scholar
  43. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293:321–331CrossRefGoogle Scholar
  44. Wuttke J (1991) Data reduction for quasielastic neutron scattering, ILL internal report 91WU08TGoogle Scholar
  45. Wuttke J (2006) FRIDA (fast reliable inelastic data analysis), http://sourceforge.net/projects/frida/
  46. Zirkel A, Roth S, Schneider W, Neuhaus J, Petry W (2000) The time-of-flight spectrometer with cold neutrons at the FRM-II. Physica B 276–278:120–121CrossRefGoogle Scholar

Copyright information

© EBSA 2008

Authors and Affiliations

  1. 1.E13, Physik DepartmentTechnische Universität MünchenGarching bei MünchenGermany
  2. 2.FRM II Forschungsneutronenquelle Heinz Maier-LeibnitzTechnische Universität MünchenGarching bei MünchenGermany

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